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FF:12151-128F9: Difference between revisions

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|creation_date=
|creation_date=
|def=
|def=
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|fonse_cell_line=
|fonse_cell_line=
|fonse_cell_line_closure=
|fonse_cell_line_closure=

Revision as of 17:21, 29 March 2012


Name:CD19+ B Cells (pluriselect), donor090325, donation1
Species:Human (Homo sapiens)
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View: UCSC
CAGEd-oPOSSUM:link
Additional information
Sample information
strainNA
tissueblood
dev stageNA
sexmale
ageNA
cell typeb cell
cell lineNA
companyNA
collaborationMatched_genome_OSC(contact:Al Forrest)
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
RNA information
lot numberNA
catalog numberNA
sample typetotal RNA
extraction protocol (Details)OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
Download raw sequence, BAM & CTSS
Hg19
BAMCTSS
[{{{hg19bam}}} download][{{{hg19ctss}}} donwload]
Hg38
BAMCTSS
[{{{hg38bam}}} download][{{{hg38ctss}}} donwload]


Relative expression to median (log10)

Transcription factors with enriched expression in this sampleRanked list of transcription factor promoter expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed.



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data

Coexpression clusterscore
C0-CD14-Eosinophils-Neutrophils-Basophils-CD34-immature-Peripheral0
C1-testis-epididymis-embryonic-medulla-pituitary-trachea-caudate0
C10-occipital-temporal-parietal-brain-duodenum-Neurons-Neural0
C100-rhabdomyosarcoma-gastric-pineal-Wilms-cervical-mesodermal-endometrial0
C101-small-cerebellum-maxillary-colon-parietal-epididymis-merkel0
C102-neuroblastoma-testicular-pituitary-carcinosarcoma-rectum-acantholytic-iPS0
C103-CD4-CD8-Natural-Peripheral-Whole-Neutrophils-Basophils0
C104-Mast-Basophils-immature-CD14-CD34-eye-Natural0
C105-heart-skeletal-occipital-hippocampus-acute-Sebocyte-penis-0.068
C106-Hep2-epitheloid-placenta-cervical-rectal-anaplastic-glassy0
C107-Neutrophils-CD14-Eosinophils-Monocytederived-Whole-Peripheral-blood0
C108-breast-hepatoblastoma-MCF7-parotid-salivary-submaxillary-prostate0
C109-Reticulocytes-non-acute-Hodgkin-Burkitt-retinoblastoma-lymphoma-0.172
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C90-neuroectodermal-peripheral-neuroepithelioma-neuroblastoma-carcinoid-parietal-putamen0
C91-Fibroblast-Smooth-mesenchymal-Mesothelial-Small-Preadipocyte-Hair0
C92-CD14CD16-CD14-Eosinophils-Basophils-Neutrophils-Macrophage-Whole0
C93-chronic-acute-leukemia-acantholytic-medulloblastoma-testis-papillotubular0
C94-smallcell-adrenal-lung-nonsmall-small-somatostatinoma-teratocarcinoma0
C95-lung-aorta-trachea-penis-Alveolar-throat-endometrioid0
C96-non-acute-tonsil-spleen-Burkitt-lymphoma-appendix0
C97-small-smallcell-gastrointestinal-argyrophil-putamen-duodenum-brain0
C98-CD8-Natural-Basophils-blood-CD4-Peripheral-Whole0
C99-hairy-mycosis-submaxillary-salivary-cord-kidney-parotid0



Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data no result for this sample


TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample

JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12531

Jaspar motifP-value
MA0002.27.69392e-5
MA0003.10.886
MA0004.10.156
MA0006.10.394
MA0007.10.554
MA0009.10.712
MA0014.10.28
MA0017.10.164
MA0018.20.0109
MA0019.10.795
MA0024.10.547
MA0025.10.815
MA0027.10.717
MA0028.11.72697e-6
MA0029.10.33
MA0030.10.00766
MA0031.10.0636
MA0035.20.927
MA0038.10.785
MA0039.20.121
MA0040.10.985
MA0041.10.209
MA0042.10.817
MA0043.10.00359
MA0046.10.59
MA0047.20.193
MA0048.10.561
MA0050.16.32324e-12
MA0051.14.66978e-6
MA0052.10.406
MA0055.10.367
MA0057.10.531
MA0058.10.0627
MA0059.10.245
MA0060.10.683
MA0061.14.57432e-10
MA0062.26.77707e-17
MA0065.20.0863
MA0066.10.611
MA0067.10.0464
MA0068.10.00122
MA0069.10.591
MA0070.10.228
MA0071.10.973
MA0072.10.829
MA0073.10.545
MA0074.10.935
MA0076.12.46711e-10
MA0077.10.17
MA0078.10.739
MA0079.20.66
MA0080.22.94931e-12
MA0081.16.90799e-5
MA0083.10.263
MA0084.10.298
MA0087.10.146
MA0088.10.0985
MA0090.19.29019e-5
MA0091.10.835
MA0092.10.62
MA0093.10.161
MA0099.21.06481e-4
MA0100.10.0758
MA0101.13.35352e-8
MA0102.20.0146
MA0103.10.0316
MA0104.20.0748
MA0105.11.85185e-9
MA0106.10.244
MA0107.12.07042e-8
MA0108.24.16751e-5
MA0111.10.409
MA0112.20.202
MA0113.10.653
MA0114.10.205
MA0115.10.428
MA0116.13.07384e-5
MA0117.10.575
MA0119.10.419
MA0122.10.414
MA0124.10.442
MA0125.10.962
MA0131.10.0167
MA0135.10.0576
MA0136.12.29257e-20
MA0137.20.414
MA0138.20.751
MA0139.10.346
MA0140.10.722
MA0141.10.718
MA0142.10.383
MA0143.10.753
MA0144.10.988
MA0145.10.243
MA0146.10.196
MA0147.10.122
MA0148.10.914
MA0149.10.229
MA0150.10.867
MA0152.10.235
MA0153.10.0122
MA0154.12.65054e-4
MA0155.10.585
MA0156.11.4178e-16
MA0157.10.128
MA0159.10.164
MA0160.10.396
MA0162.10.986
MA0163.11.33777e-6
MA0164.10.676
MA0258.10.339
MA0259.10.483



FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: CNhs12531

Novel motifP-value
10.183
100.0267
1000.487
1010.386
1020.958
1030.782
1040.211
1050.365
1060.683
1070.12
1080.133
1090.114
110.239
1100.341
1110.207
1120.412
1130.0451
1140.693
1150.775
1160.671
1174.47247e-4
1180.179
1190.957
120.823
1200.648
1210.209
1220.621
1230.0251
1240.534
1250.125
1260.218
1270.971
1280.313
1290.332
130.287
1300.461
1310.584
1320.338
1330.04
1340.463
1350.674
1360.215
1370.0131
1380.402
1390.203
140.301
1400.777
1410.451
1420.544
1430.236
1440.661
1450.189
1460.333
1470.0325
1480.304
1490.817
150.204
1500.877
1510.832
1520.794
1530.861
1540.909
1550.0189
1560.733
1570.227
1580.237
1590.0817
160.542
1600.845
1610.224
1620.188
1630.39
1640.239
1650.18
1660.515
1670.104
1680.25
1690.882
170.741
180.752
190.465
20.356
200.184
210.841
220.941
230.489
240.7
250.0277
260.339
270.819
280.343
290.0417
30.066
300.144
310.919
320.0965
330.355
340.937
350.193
360.0399
370.0905
380.486
390.408
40.912
400.214
410.133
420.135
430.27
440.953
450.801
460.538
470.132
480.328
490.192
50.469
500.983
510.762
520.545
530.368
540.979
550.366
560.827
570.765
580.05
590.858
60.742
600.494
610.0492
620.125
630.812
640.538
650.965
660.897
670.219
680.524
690.67
70.136
700.355
710.0562
720.0335
730.428
740.31
750.00292
760.025
770.283
780.284
790.327
80.855
800.0121
810.204
820.427
830.971
840.16
850.723
860.0577
870.0544
880.728
890.401
90.767
900.0977
910.637
920.855
930.985
940.0827
950.00472
960.773
970.603
980.335
990.00383



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: CNhs12531


FANTOM5 (FF) ontology

Direct parent terms


Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
0000000 (cell), 0000000 (cell)
0000003 (native cell)
0000034 (stem cell)
0000037 (hematopoietic stem cell)
0000048 (multi fate stem cell)
0000051 (common lymphoid progenitor)
0000134 (mesenchymal cell)
0000219 (motile cell)
0000236 (B cell)
0000255 (eukaryotic cell)
0000542 (lymphocyte)
0000548 (animal cell)
0000566 (angioblastic mesenchymal cell)
0000723 (somatic stem cell)
0000738 (leukocyte)
0000826 (pro-B cell)
0000837 (hematopoietic multipotent progenitor cell)
0000838 (lymphoid lineage restricted progenitor cell)
0000945 (lymphocyte of B lineage)
0000988 (hematopoietic cell)
0002031 (hematopoietic lineage restricted progenitor cell)
0002032 (hematopoietic oligopotent progenitor cell)
0002087 (nongranular leukocyte)
0002320 (connective tissue cell)
0002371 (somatic cell)

UBERON: Anatomy
0000061 (anatomical structure)
0000465 (material anatomical entity)
0000479 (tissue)
0001062 (anatomical entity)
0002384 (connective tissue)

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA

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